Weellll... I suppose there is nothing wrong with a Magical Girl character not being cute... but I personally believe she should be... or at least make her elegant or beautiful or maybe dignified. There is no strict boundary, but I think you more or less get the image of what I'm trying to say ;_;
EDIT: Just realized that actually that's not necessary. But make the girl likable. Fans of Magical Girl genre want to like the girls! If you want to make a muscular tomboy magical girl, make her likably burly.
It doesn't really break any law to make a magical girl that doesn't transform either; but for most Mahou Shoujo fans, a magical girl transformation is one of the biggest appeal ;)
As for plot... that's how it originally went. Mahou Shoujo originally is about cute girls fighting against evil. Stories about friendship and love and everything wonderful. That is... at least until a magical girl show dedicated to deconstruct it appeared in 2011: Madoka Magica -- an extremely dark Magical Girl show (won't spoil it you should watch it it's extremely awesome). Since then magical girl shows inspired by Madoka has appeared -- which turns Mahou Shoujo into some quite dark shows - some good but some missed the point. But the point is now magical girl shows with extremely grim stories exist. For example Magical Girl Raising Project is about magical girls killing each other.
Anyway, still good work. Thanks for participating :D
P.S. I just realized though... you figured out that the hidden side themes had to do with Magia Record. I never mentioned the name of the anime in my other discussion yet you figured it out. I'm actually surprised you are not familiar with the Magical Girl genre